Paper Citing NAMD - Abstract
Murciano-Calles, Javier; Corbi-Verge, Carles; Candel, Adela M.; Luque, Irene; Martinez, Jose C.
Post-Translational Modifications Modulate Ligand Recognition by the Third PDZ Domain of the MAGUK Protein PSD-95
PLOS ONE, 9 Art. No. e90030, FEB 26 2014
The relative promiscuity of hub proteins such as postsynaptic density protein-95 (PSD-95) can be achieved by alternative splicing, allosteric regulation, and post-translational modifications, the latter of which is the most efficient method of accelerating cellular responses to environmental changes in vivo. Here, a mutational approach was used to determine the impact of phosphorylation and succinimidation post-translational modifications on the binding affinity of the postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ3) domain of PSD-95. Molecular dynamics simulations revealed that the binding affinity of this domain is influenced by an interplay between salt-bridges linking the alpha 3 helix, the beta 2-beta 3 loop and the positively charged Lys residues in its high-affinity hexapeptide ligand KKETAV. The alpha 3 helix is an extra structural element that is not present in other PDZ domains, which links PDZ3 with the following SH3 domain in the PSD-95 protein. This regulatory mechanism was confirmed experimentally via thermodynamic and NMR chemical shift perturbation analyses, discarding intra-domain long-range effects. Taken together, the results presented here reveal the molecular basis of the regulatory role of the alpha 3 extra-element and the effects of post-translational modifications of PDZ3 on its binding affinity, both energetically and dynamically.
